kmg plot #141

shajoezhu · 2025-11-28T05:48:03Z

What changes are proposed in this pull request?

Style this entry in a way that can be copied directly into NEWS.md. (#, @)

Provide more detail here as needed.

Reference GitHub issue associated with pull request. e.g., 'closes #'

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PR branch has pulled the most recent updates from master branch: usethis::pr_merge_main()
If a bug was fixed, a unit test was added.
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Request a reviewer

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If a bug was fixed, a unit test was added.
Run pkgdown::build_site(). Check the R console for errors, and review the rendered website.
Code coverage is suitable for any new functions/features: devtools::test_coverage()

When the branch is ready to be merged:

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shajoezhu · 2025-11-28T05:48:31Z

try and use exisitng structure and surv functions, refactoring will be addressed in #142

github-actions · 2025-11-28T05:52:05Z

Unit Tests Summary

1 files 71 suites 1m 28s ⏱️
71 tests 71 ✅ 0 💤 0 ❌
179 runs 179 ✅ 0 💤 0 ❌

Results for commit 67f9bcf.

♻️ This comment has been updated with latest results.

github-actions · 2025-11-28T05:52:08Z

Unit Test Performance Difference

Test Suite	$Status$	Time on `main`	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
gkm	👶		$+0.05$	$+3$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on `main`	$±Time$	Test Case
gkm	👶		$+0.05$	test_gkm_works

Results for commit 45fde37

♻️ This comment has been updated with latest results.

github-actions · 2025-11-28T05:52:37Z

Code Coverage Summary

Filename                               Stmts    Miss  Cover    Missing
-----------------------------------  -------  ------  -------  ----------------------------------------------------------------------------------------------------
R/add_blank_rows.R                        63       0  100.00%
R/add_difference_row.R                   101       0  100.00%
R/add_hierarchical_count_row.R            33       0  100.00%
R/crane-package.R                          2       2  0.00%    27-28
R/deprecated.R                             6       6  0.00%    15-21
R/gg_km_utils.R                          119      17  85.71%   46, 103-120, 136, 199
R/gg_km.R                                220      40  81.82%   50-53, 70, 97, 186-188, 192-199, 222-224, 231-234, 238, 249-253, 266, 268-270, 284, 287-289, 405-409
R/label_roche.R                           72       0  100.00%
R/modify_header_rm_md.R                   18       2  88.89%   35-36
R/modify_zero_recode.R                    13       0  100.00%
R/tbl_baseline_chg.R                     186       0  100.00%
R/tbl_hierarchical_rate_and_count.R      148       0  100.00%
R/tbl_hierarchical_rate_by_grade.R       271       3  98.89%   162-164
R/tbl_listing.R                           35       0  100.00%
R/tbl_null_report.R                        9       0  100.00%
R/tbl_roche_summary.R                     64       0  100.00%
R/tbl_shift.R                            116       0  100.00%
R/tbl_survfit_quantiles.R                132       1  99.24%   295
R/tbl_survfit_times.R                     92       0  100.00%
R/theme_gtsummary_roche.R                 74       0  100.00%
R/utils.R                                 36       0  100.00%
TOTAL                                   1810      71  96.08%

Diff against main

Filename           Stmts    Miss  Cover
---------------  -------  ------  -------
R/gg_km_utils.R     +119     +17  +85.71%
R/gg_km.R           +220     +40  +81.82%
TOTAL               +339     +57  -2.97%

Results for commit: 67f9bcf

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

shajoezhu · 2025-11-28T15:19:49Z

need examples and export
h_km_fit, h_tbl_coxph_pairwise,

…to adding_g_km

shajoezhu · 2025-11-30T02:54:15Z

my styler is failing, @edelarua , i was wondering how you guys check style here https://github.com/insightsengineering/crane/actions/runs/19792793759/job/56708402248?pr=141

shajoezhu · 2025-11-30T02:55:43Z

checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'annot_cox_ph.Rd':
‘control_coxph_annot’

Missing link(s) in Rd file 'annot_surv_med.Rd':
‘control_surv_med_annot’

Missing link(s) in Rd file 'h_tbl_coxph_pairwise.Rd':
‘control_coxph’

Missing link(s) in Rd file 's_coxph_pairwise.Rd':
‘control_coxph’

See section 'Cross-references' in the 'Writing R Extensions' manual.

checking for missing documentation entries ... WARNING
Undocumented code objects:
‘obj_label’
Undocumented S4 methods:
generic 'obj_label' and siglist 'ANY'
generic 'obj_label<-' and siglist 'ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'obj_label-set.Rd'
‘obj’

R/gkm.R

R/crane-package.R

R/gkm.R

Melkiades · 2025-12-04T09:40:52Z

DESCRIPTION

+    cowplot (>= 1.2.0),
+    checkmate (>= 2.3.2),


I think we do not need checkmate AND assertthat. Also I would not add them as we do not need them in nest 2.0 (bad error messaging)

Melkiades · 2025-12-04T09:42:11Z

R/gg_km.R

+#' annot_cox_ph(plt_kmg01, coxph_tbl)
+#'
+annot_cox_ph <- function(gg_plt, coxph_tbl, control_annot_coxph = control_coxph_annot(), font_size = 10) {
+  # ... (function body remains the same)


what does this mean?

can remove this line

Melkiades · 2025-12-04T09:43:54Z

R/gkm.R

+g_km <- function(
+  surv_plot_data,
+  col = NULL,
+  lty = NULL,
+  lwd = 0.5,
+  censor_show = TRUE,
+  pch = 3,
+  size = 2,
+  max_time = NULL,
+  xticks = NULL,
+  xlab = "Days",
+  yval = c("Survival", "Failure"),
+  ylab = paste(yval, "Probability"),
+  ylim = NULL,
+  title = NULL,
+  footnotes = NULL,
+  font_size = 10,
+  ci_ribbon = FALSE,
+  legend_pos = NULL,
+  ggtheme = NULL
+) {


too many parameters imo

Melkiades · 2025-12-04T09:45:59Z

R/gkm.R

+#' @param surv_plot_data A data frame containing the pre-processed survival data, ready for plotting.
+#'   This data should be equivalent to the output of \code{h_data_plot}.
+#' @param col A character vector of colors for the survival curves. Length should match number of arms.
+#' @param lty A vector of line types for the survival curves, or \code{NULL} for default.
+#' @param lwd Numeric value specifying line width for the survival curves.
+#' @param censor_show Logical, whether to display censoring marks on the plot.
+#' @param pch Plotting character for censoring marks.
+#' @param size Size of the censoring marks.
+#' @param max_time Numeric, the maximum time point to display on the x-axis.
+#' @param xticks Numeric vector of x-axis tick positions, or a single number for the interval, or \code{NULL} for auto.
+#' @param xlab Character string for the x-axis label.
+#' @param yval Character string, either \code{"Survival"} or \code{"Failure"} to plot Survival or Failure probability.
+#' @param ylab Character string for the y-axis label.
+#' @param ylim Numeric vector of length 2 for y-axis limits.
+#' @param title Character string for the plot title.
+#' @param footnotes Character string for plot footnotes/caption.
+#' @param font_size Numeric, base font size for the plot theme.
+#' @param ci_ribbon Logical, whether to display confidence intervals as a ribbon (area).
+#' @param legend_pos Numeric vector of length 2 for legend position (x, y) relative to the plot area (0 to 1), or \code{NULL} for auto-placement.


parameter description does not reflect the rest of the package standard

Melkiades · 2025-12-04T09:50:07Z

R/gkm.R

+      xend = tot_width - 0.1 * tail(colwidths, 1), y = nrow(df) -
+        0.5, yend = nrow(df) - 0.5


I think we need to style this a bit

Melkiades · 2025-12-04T09:51:50Z

R/gkm.R

+    current_row <- data.frame(
+      hr = sprintf("%.2f", coxph_ans$conf.int[1, 1]),


we should use glue

R/crane-package.R

shajoezhu · 2025-12-06T10:11:26Z

hi davide, can you fix the test please https://github.com/insightsengineering/crane/actions/runs/19936180249/job/57161536238 thanks

init commit

70ec9a0

Merge branch 'main' into adding_g_km

105a6dc

shajoezhu added 8 commits November 28, 2025 23:39

update

6d8d156

Merge branch 'adding_g_km' of github.com:insightsengineering/crane in…

c3bbe60

…to adding_g_km

wip

41b7497

wordlist

9b8807a

adding code

6b51033

update ad test

2912448

update namespace

015b86e

update doc

ec08202

shajoezhu mentioned this pull request Nov 30, 2025

g_km refactoring #142

Open

3 tasks

shajoezhu added 12 commits December 1, 2025 09:43

rm code

585ee24

rm doc

4c3268f

modify code

b29d65d

update

44b191c

updat epkgdown

770c10b

restyle:

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update

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update test

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update doc

1e3fa5d

not using ggsurvfit yet

de896d3

restyle test

c65cf11

update assertion

4364b7a

shajoezhu added 4 commits December 1, 2025 19:35

update assertion

065ca7d

update test

889c21a

update

afebed3

update

8f52316

Melkiades reviewed Dec 1, 2025

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shajoezhu added 7 commits December 1, 2025 22:33

manual vbump

d5a79b7

rm assertion

fcafc3e

resolve conflict

f6b2b36

reorg code

7dd95f0

adding example

5dfacdd

updatedoc

6f0f048

fix eg

1d63f4b

shajoezhu requested a review from Melkiades December 3, 2025 04:50

Melkiades reviewed Dec 4, 2025

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shajoezhu changed the title ~~init commit~~ kmg plot Dec 4, 2025

changes

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Melkiades marked this pull request as draft December 4, 2025 15:50

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Melkiades added 2 commits December 4, 2025 17:24

removing more parameters

e100634

change name

452e26c

		xend = tot_width - 0.1 * tail(colwidths, 1), y = nrow(df) -
		0.5, yend = nrow(df) - 0.5

		current_row <- data.frame(
		hr = sprintf("%.2f", coxph_ans$conf.int[1, 1]),

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